Neon Genesis Evangelion: It has invokes tons of strong emotions both positive and negative throughout, but I don't think anything has affected me quite as much Asuka's battle with the Mass Production Evas in End of Evangelion, especially towards the end. I literally cannot listen to the Bach piece "Air" without thinking of this battle and getting a bit depressed.

Fate Zero: Rider's glorious charge against Archer, including Waver's reaction after the battle. Also the ending of the show in the way it set things up for Fate Stay Night, I'd say it's a feeling of absolute completeness.

Wolf's Rain, no doubt. I can't even begin to describe the emotions it made me feel. You could almost say it was a life-changing experience.5cm per second, also another powerful one. Like Wolf's Rain it's so... life-changing. No other way to describe it, really.

I'm trying to think of anything else, but nothing's coming at the moment. I'll probably remember something else later

SAO, epic, depressing, anger, rage, love, it's crazy
shuffle, I KNOW!!! last episodes are so so so so so so so... :.) i'm going to watch it again
toradora, the best kiss scene in moving picture history, yes i am being biased
belle & sebastian, i miss that dog
eureka seven was pretty awesome
claymore had it's moments

The really sweet moments between Teito and Mikage, the pain of Mikage and Bastien's deaths, the amusing moments between Frau and other characters. I feel like every episode of the anime managed to hit the whole range of emotions.